There's a lot of good options for intake plenums and TB's. Lots of people have different opinions of which size is better too. Personally, I recommend the BBK 78mm TB/Plenum
for your GT.
Now, I don't want to give you the wrong impression, bigger is not always better. However, the BBK 78mm TB/Plenum has worked very well on every 2v GT I've seen sporting it. We even equipped our own N/A '00 GT with the same combo and saw significant gains throughout the entire power curve! Plus, another very attractive feature of this setup is the price. You'll save just about half the cash it would cost you to run an Acufab TB & upper, while both options yield similar results.
You can check out a video of our '00 GT on the dyno at the link below. I think you'll be very impressed with the overall HP/TQ gains shown on our in house DynoJet 224xLC. Also, if you have any more questions, feel free to ask me. I'd be happy to help anyway possible!
1999-2004 Mustang GT Power Pack - AmericanMuscle Bolt-On Build-Ups - YouTube